Hands-On Training
Protégé Short Course
June 23–25, 2026
Stanford, California, USA
This two-and-a-half day Protégé Short Course provides a comprehensive introduction to ontology development and the OWL 2 Web Ontology Language using the Protégé toolset. Most of the course is hands-on. Participants will learn how to navigate the latest version of the Protégé and WebProtégé toolsets, which support the full OWL 2 standard.
The course is taught by members of the Protégé team. Enrollment is limited to ensure optimal learning experiences.
Target audience members include everyone who wishes to develop or enhance their skills for building OWL ontologies using Protégé. The course can benefit both beginners with no prior experience and intermediate users of Protégé Desktop or WebProtégé.
Topics
- ✓ Steps in the ontology development process
- ✓ Semantic Web technologies, e.g., OWL and RDF
- ✓ OWL 2 language, reasoning, and querying
- ✓ Collaborative ontology development
- ✓ Import from spreadsheets and other data sources
Detailed topic list
Introduction to Ontologies and Ontology Engineering
- Knowledge Representation on the Web: Motivation and examples
- Definitions of ontology
- Rationale for ontologies: why build ontologies, example applications and usage
- Basic components of an ontology
- Introduction to course running example
- Knowledge Engineering Techniques: defining domain and scope, competency questions, card sorting, identifying domain terms
- Ontology modeling approaches: generic and application ontologies, ontology design patterns
- Testing ontologies: competency questions as tests, validation strategies
Introduction to Protégé
- The Protégé user interface: tabs, views, lists and sections
Introduction to OWL
- Where OWL fits into the Knowledge Representation landscape
- Basic OWL terminology: Classes, Object Properties, Data Properties, Annotation Properties, Individuals, Datatypes, Literals, Complex Class Expressions, Axioms
- Entailment, Inference and Automated Reasoning
- OWL Profiles (OWL2EL, OWL2QL and OWL2RL)
- The Resource Description Framework (RDF)
- OWL Syntaxes and the relationship to RDF
Hands on OWL
- Entities and entity naming strategies
- Classes: declarations, owl:Thing, owl:Nothing
- SubClassOf axioms, class hierarchies and terminology
- Entailment, reasoning, and automated computation of class hierarchies
- Annotation assertions for metadata: literals, language tags, referencing external information, working with SKOS and Schema.org
- Representing relationships at the class level: object properties, SomeValuesFrom (existential restrictions), property hierarchies, HasValueFrom
- Transitive property axioms
- Functional properties
- Combining complex class expressions: IntersectionOf (And), UnionOf (Or), OneOf (Enumerations)
- Class definitions: EquivalentClasses axioms, primitive and defined classes
- Negation in OWL: ComplementOf (Not), disjoint classes axioms
- Negation of complex class expressions, AllValuesFrom (universal restrictions), and the duality with SomeValuesFrom
- Representing relationships at the instance level: individuals, PropertyAssertion axioms, property chains, domain and range axioms
- Data properties and data ranges
- Understanding the Open World Assumption (OWA)
Who tends to attend
Enrollment is capped to keep the group small enough for meaningful interaction with the instructors and with each other. The mix varies from year to year, but cohorts typically draw an international audience and tend to include:
- ✓ Biomedical and life-science researchers building or applying ontologies for clinical, disease, phenotype, drug, or data-harmonization work.
- ✓ Knowledge engineers and ontologists designing, maintaining, or integrating ontologies and knowledge graphs.
- ✓ Industry professionals applying ontologies to practical problems — including Silicon Valley tech companies, and across pharma, biotech and healthcare; finance and insurance; software and AI; and government, defense and standards bodies.
- ✓ Graduate students and postdoctoral researchers seeking formal training in ontology development.
- ✓ Librarians, terminologists, and standards staff working on controlled vocabularies and terminology services also join from time to time.
Past cohorts have included participants from universities, research institutes, industry, government agencies, and international organizations such as the World Health Organization (WHO).
The result is a rich and unique experience. Participants learn content, and learn it in a way, that is hard to find anywhere else — the combination of instructors, materials, hands-on modeling work, and the format of the course is not easily replicated through online tutorials, books, or self-study.
Much of that value comes from the mix of people in the room. Working alongside peers from different disciplines and sectors deepens understanding of the material, broadens the range of real-world modeling problems and approaches participants encounter, and helps attendees build professional contacts that often last well beyond the course itself.
Peek Inside
A 221-page hands-on companion, exclusive to participants
Written by the Protégé team for this course and available only to those who attend. The book is yours to take home and return to long after the course ends. Inside: 23 chapters, 111 hands-on exercises, fill-in sections you complete as you go, and quizzes to test your understanding — all illustrated with diagrams, step-by-step Protégé walkthroughs, and modelling discussions you won't find anywhere else.
★ One of the unique benefits of attending
Fees
Early Bird — register by May 23
Regular
$2,150
$2,300 after May 23
Student
$350
$400 after May 23
Fees include lunch, course materials, and a comprehensive 221-page course manual packed with hands-on exercises, diagrams, and in-depth coverage of OWL, the Protégé user interface, and ontology modeling.
The student rate requires proof of current enrollment at a higher education institution. Registration at the student rate will only be approved after documentation has been submitted.
Cancellation Policy
If you cancel by the dates below, your registration fee will be refunded minus the applicable cancellation fee. The same fees apply to both regular and student registrations.
| Cancel by | Regular | Student |
|---|---|---|
| May 23, 2026 | $100 | $100 |
| June 9, 2026 | $200 | $200 |
Cancellations received after June 9, 2026 are non-refundable.
Venue
3180 Porter Drive
Room B107
Palo Alto, California 94304
USA
Stanford Research Park
The main entrance to the 3180 Porter Drive building is at the rear of the building. (The entrance at the front of the building is locked and only accessible with a keycard).
Travel
Parking
You can park for free around the back of the 3180 Porter Drive building where the course will be held.
Shuttle
Stanford provides a free Shuttle Service for getting around the campus, known as "The Marguerite". The Research Park line (RP) stops in front of the 3170 Porter Drive building where the course will be held.
Hotels
Preparation
Please download and install the latest version of Protégé Desktop (version 5.6.8 or later) before the course begins.
A laptop is required for hands-on exercises. Please ensure your laptop is fully charged and that you bring a power adapter.
Schedule
The detailed schedule will be posted closer to the course date. Here is a general outline of what to expect:
Day 1
Introduction to ontologies, knowledge engineering techniques, and getting started with Protégé and OWL
Day 2
Deeper into OWL: class expressions, reasoning, and hands-on modeling exercises
Day 3 (half day)
Collaborative ontology development with WebProtégé, advanced topics, and open discussion
FAQ
Do I need prior experience with ontologies?
No. The course is designed for beginners through intermediate users.
What should I bring?
A laptop with the latest version of Protégé Desktop installed, and a power adapter.
Is lunch provided?
Yes. Lunch, course materials, and a comprehensive 221-page course manual are all included. The manual is packed with hands-on exercises, diagrams, and in-depth coverage of OWL, the Protégé user interface, and ontology modeling.
What is the cancellation policy?
Your registration fee is refunded minus a cancellation fee: $100 if cancelled by May 23, 2026, or $200 if cancelled by June 9, 2026. Cancellations received after June 9, 2026 are non-refundable. See the full cancellation policy for details.